switching AJA to INSERT method, dealing with collisions via API

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -63,7 +63,7 @@ sub default_table_name {
 
 
 sub default_insertion_method {
-    return 'INSERT_IGNORE';
+    return 'INSERT';
 }
 
 
@@ -125,6 +125,39 @@ sub fetch_by_analysis_id_and_input_id {     # It is a special case not covered b
 }
 
 
+sub class_specific_execute {
+    my ($self, $object, $sth, $values) = @_;
+
+    my $return_code;
+
+    eval {
+        $return_code = $self->SUPER::class_specific_execute($object, $sth, $values);
+        1;
+    } or do {
+        my $duplicate_regex = {
+            'mysql'     => qr/Duplicate entry.+?for key/s,
+            'sqlite'    => qr/columns.+?are not unique|UNIQUE constraint failed/s,  # versions around 3.8 spit the first msg, versions around 3.15 - the second
+            'pgsql'     => qr/duplicate key value violates unique constraint/s,
+        }->{$self->db->dbc->driver};
+
+        if( $@ =~ $duplicate_regex ) {      # implementing 'INSERT IGNORE' of Jobs on the API side
+            my $emitting_job_id = $object->prev_job_id;
+            my $analysis_id     = $object->analysis_id;
+            my $input_id        = $object->input_id;
+            my $msg             = "Attempt to insert a duplicate job (analysis_id=$analysis_id, input_id=$input_id) intercepted and ignored";
+
+            $self->db->get_LogMessageAdaptor->store_job_message( $emitting_job_id, $msg, 'INFO' );
+
+            $return_code = '0E0';
+        } else {
+            die $@;
+        }
+    };
+
+    return $return_code;
+}
+
+
 =head2 store_jobs_and_adjust_counters
 
   Arg [1]    : arrayref of Bio::EnsEMBL::Hive::AnalysisJob $jobs_to_store

modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm

@@ -502,6 +502,15 @@ sub check_object_present_in_db_by_content {    # return autoinc_id/undef if the
 }
 
 
+sub class_specific_execute {
+    my ($self, $object, $sth, $values) = @_;
+
+    my $return_code = $sth->execute( @$values );
+
+    return $return_code;
+}
+
+
 sub store {
     my ($self, $object_or_list) = @_;
 
@@ -546,9 +555,10 @@ sub store {
             my $values_being_stored = $self->slicer( $object, $columns_being_stored );
             # warn "STORED_VALUES: ".stringify($values_being_stored)."\n";
 
-            my $return_code = $this_sth->execute( @$values_being_stored )
+            my $return_code = $self->class_specific_execute($object, $this_sth, $values_being_stored )
                     # using $return_code in boolean context allows to skip the value '0E0' ('no rows affected') that Perl treats as zero but regards as true:
                 or throw("Could not store fields\n\t{$column_key}\nwith data:\n\t(".join(',', @$values_being_stored).')');
+
             if($return_code > 0) {     # <--- for the same reason we have to be explicitly numeric here
                 my $liid = $autoinc_id && $self->dbc->db_handle->last_insert_id(undef, undef, $table_name, $autoinc_id);
                 $self->mark_stored($object, $liid );

sql/tables.pgsql

@@ -369,6 +369,7 @@ CREATE TABLE job (
 CREATE INDEX ON job (analysis_id, status, retry_count); -- for claiming jobs
 CREATE INDEX ON job (role_id, status);                  -- for fetching and releasing claimed jobs
 
+/*
 -- PostgreSQL is lacking INSERT IGNORE, so we need a RULE to silently
 -- discard the insertion of duplicated entries in the job table
 CREATE OR REPLACE RULE job_table_ignore_duplicate_inserts AS
@@ -378,6 +379,7 @@ CREATE OR REPLACE RULE job_table_ignore_duplicate_inserts AS
 	FROM job
 	WHERE job.input_id=NEW.input_id AND job.param_id_stack=NEW.param_id_stack AND job.accu_id_stack=NEW.accu_id_stack AND job.analysis_id=NEW.analysis_id)
     DO INSTEAD NOTHING;
+*/
 
 /**
 @table  job_file